Refactoring codes for removing buffer size options. An some other changes...

Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
2025-06-29 16:20:46 +00:00 · 2023-03-07 11:12:13 +07:00
parent 9811e440b8
commit d88de15cdc
52 changed files with 1172 additions and 421 deletions
--- a/doc/book/annexes.qmd
+++ b/doc/book/annexes.qmd
@ -1,82 +1,107 @@
 # Annexes

-### Sequence attributes
+## Sequence attributes

-#### Reserved sequence attributes
+**ali_dir (`string`)**

-##### `ali_dir`
+  - Set by the *obipairing* tool
+  - The attribute can contain 2 string values `left` or `right`.

-###### Type : `string`
+  The alignment generated by *obipairing* is a 3'-end gap free algorithm.
+  Two cases can occur when aligning the forward and reverse reads. If the
+  barcode is long enough, both the reads overlap only on their 3' ends. In
+  such case, the alignment direction `ali_dir` is set to *left*. If the
+  barcode is shorter than the read length, the paired reads overlap by
+  their 5' ends, and the complete barcode is sequenced by both the reads.
+  In that later case, `ali_dir` is set to *right*.

-The attribute can contain 2 string values `"left"` or `"right".`
+**ali_length (`int`)**

-###### Set by the *obipairing* tool
+  - Set by the *obipairing* tool

-The alignment generated by *obipairing* is a 3'-end gap free algorithm.
-Two cases can occur when aligning the forward and reverse reads. If the
-barcode is long enough, both the reads overlap only on their 3' ends. In
-such case, the alignment direction `ali_dir` is set to *left*. If the
-barcode is shorter than the read length, the paired reads overlap by
-their 5' ends, and the complete barcode is sequenced by both the reads.
-In that later case, `ali_dir` is set to *right*.
+  Length of the aligned parts when merging forward and reverse reads

-##### `ali_length`

-###### Set by the *obipairing* tool
+**count (`int`)**

-Length of the aligned parts when merging forward and reverse reads
+  - Set by the *obiuniq* tool
+  - Getter : method `Count()`
+  - Setter : method `SetCount(int)`

-##### `count` : the number of sequence occurrences
+  The `count` attribute indicates how-many strictly identical reads
+  have been merged in a single record. It contains an integer value. If it
+  is absent this means that the sequence record represents a single
+  occurrence of the sequence.

-###### Set by the *obiuniq* tool
+  The `Count()` method allows to access to the count attribute as an
+  integer value. If the `count` attribute is not defined for the given
+  sequence, the value *1* is returned

-The `count` attribute indicates how-many strictly identical sequences
-have been merged in a single record. It contains an integer value. If it
-is absent this means that the sequence record represents a single
-occurrence of the sequence.
+**merged_* (`map[string]int`)**

-###### Getter : method `Count()`
+  - Set by the *obiuniq* tool

-The `Count()` method allows to access to the count attribute as an
-integer value. If the `count` attribute is not defined for the given
-sequence, the value *1* is returned
+  The `-m` option of the *obiuniq* tools allows for keeping track of the
+  distribution of the values stored in given attribute of interest. Often
+  this option is used to summarise distribution of a sequence variant
+  accross samples when *obiuniq* is run after running *obimultiplex*. The
+  actual name of the attribute depends on the name of the monitored
+  attribute. If `-m` option is used with the attribute *sample*, then this
+  attribute names *merged_sample*.

-##### `merged_*`
+**mode (`string`)**

-###### Type : `map[string]int`
+  - Set by the *obipairing* tool
+  - The attribute can contain 2 string values `join` or `alignment`.

-###### Set by the *obiuniq* tool

-The `-m` option of the *obiuniq* tools allows for keeping track of the
-distribution of the values stored in given attribute of interest. Often
-this option is used to summarise distribution of a sequence variant
-accross samples when *obiuniq* is run after running *obimultiplex*. The
-actual name of the attribute depends on the name of the monitored
-attribute. If `-m` option is used with the attribute *sample*, then this
-attribute names *merged_sample*.
+**obitag_ref_index (`map[string]string`)**

-##### `mode`
+  - Set by the *obirefidx* tool.

-###### Set by the *obipairing* tool
+  It resumes to which taxonomic annotation a match to that sequence must
+  lead according to the number of differences existing between the query
+  sequence and the reference sequence having that tag. 

-**`obitag_ref_index`**
+```json
+   {"0":"9606@Homo sapiens@species",
+    "2":"207598@Homininae@subfamily",
+    "3":"9604@Hominidae@family",
+    "8":"314295@Hominoidea@superfamily",
+    "10":"9526@Catarrhini@parvorder",
+    "12":"1437010@Boreoeutheria@clade",
+    "16":"9347@Eutheria@clade",
+    "17":"40674@Mammalia@class",
+    "22":"117571@Euteleostomi@clade",
+    "25":"7776@Gnathostomata@clade",
+    "29":"33213@Bilateria@clade",
+    "30":"6072@Eumetazoa@clade"}
+```

-###### Set by the *obirefidx* tool.
+**pairing_mismatches (`map[string]string`)**

-It resumes to which taxonomic annotation a match to that sequence must
-lead according to the number of differences existing between the query
-sequence and the reference sequence having that tag.
+  - Set by the *obipairing* tool

-###### Getter : method `Count()`
+**seq_a_single (`int`)**

-##### `pairing_mismatches`
+  - Set by the *obipairing* tool

-###### Set by the *obipairing* tool
+**seq_ab_match (`int`)**

-##### `score`
+  - Set by the *obipairing* tool

-###### Set by the *obipairing* tool
+**seq_b_single (`int`)**

-##### `score_norm`
+  - Set by the *obipairing* tool

-###### Set by the *obipairing* tool
+**score (`int`)**
+
+  - Set by the *obipairing* tool
+
+**score_norm (`float`)**
+
+  - Set by the *obipairing* tool
+  - The value ranges between 0 and 1.
+
+  Score of the alignment between forward and reverse reads expressed as a fraction of identity.
+ 
--- a/doc/book/comm_sampling.qmd
+++ b/doc/book/comm_sampling.qmd
@ -10,13 +10,39 @@

 Sequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.

+**Selection based on the sequence**
+
+
+Sequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (*e.g* `AACCTT`). But the usage of regular patterns allows for looking for more complex pattern. As example, `A[TG]C+G` matches a `A`, followed by a `T` or a `G`, then one or several `C` and endly a `G`.
+
+{{< include ../lib/options/selection/_sequence.qmd >}}
+
+*Examples:*
+
+: Selects only the sequence records that contain an *EcoRI* restriction site.
+
+```bash   
+obigrep -s 'GAATTC' seq1.fasta > seq2.fasta
+```
+    
+: Selects only the sequence records that contain a stretch of at least 10 ``A``.    
+    
+```bash   
+obigrep -s 'A{10,}' seq1.fasta > seq2.fasta
+```
+
+: Selects only the sequence records that do not contain ambiguous nucleotides.
+    
+```bash   
+obigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta
+```


 {{< include ../lib/options/selection/_min-count.qmd >}}

 {{< include ../lib/options/selection/_max-count.qmd >}}

-Example
+*Examples*

 : Selecting sequence records representing at least five reads in the dataset.

--- a/doc/book/expressions.qmd
+++ b/doc/book/expressions.qmd
@ -11,26 +11,64 @@ Several OBITools (*e.g.* obigrep, obiannotate) allow the user to specify some si

 ### Instrospection functions {.unnumbered}

- `len(x)`is a generic function allowing to retreive the size of a object. It returns 
+**`len(x)`**
+
+: It is a generic function allowing to retreive the size of a object. It returns 
  the length of a sequences, the number of element in a map like `annotations`, the number
  of elements in an array. The reurned value is an `int`.

 ### Cast functions {.unnumbered}

- `int(x)`  converts if possible the `x` value to an integer value. The function 
+**`int(x)`**  
+
+: Converts if possible the `x` value to an integer value. The function 
  returns an `int`.
- `numeric(x)` converts if possible the `x` value to a float value. The function 
+
+**`numeric(x)`** 
+
+: Converts if possible the `x` value to a float value. The function 
  returns a `float`.
- `bool(x)` converts if possible the `x` value to a boolean value. The function 
+
+**`bool(x)`** 
+
+: Converts if possible the `x` value to a boolean value. The function 
  returns a `bool`.

 ### String related functions {.unnumbered}

- `printf(format,...)` allows to combine several values to build a string. `format` follows the
+**`printf(format,...)`** 
+
+: Allows to combine several values to build a string. `format` follows the
   classical C `printf` syntax. The function returns a `string`.
- `subspc(x)` substitutes every space in the `x` string by the underscore (`_`) character. The function 
+
+**`subspc(x)`** 
+
+: substitutes every space in the `x` string by the underscore (`_`) character. The function 
   returns a `string`. 

+### Condition function {.unnumbered}
+
+**`ifelse(condition,val1,val2)`**
+
+: The `condition` value has to be a `bool` value. If it is `true` the function returns `val1`,
+  otherwise, it is returning `val2`.
+
+### Sequence analysis related function
+
+**`composition(sequence)`**
+
+: The nucleotide composition of the sequence is returned as as map indexed by `a`, `c`, `g`, or `t` and
+  each value is the number of occurrences of that nucleotide. A fifth key `others` accounts for
+  all others symboles.  
+
+**`gcskew(sequence)`**
+
+: Computes the excess of g compare to c of the sequence, known as the GC skew.
+
+    $$
+    Skew_{GC}=\frac{G-C}{G+C}
+    $$
+    
 ## Accessing to the sequence annotations

 The `annotations` variable is a map object containing all the annotations associated to the currently processed sequence. Index of the map are the attribute names. It exists to possibillities to retreive
@ -53,4 +91,7 @@ Special attributes of the sequence are accessible only by dedicated methods of t
 - The sequence identifier : `Id()`
 - THe sequence definition : `Definition()`

+```go
+sequence.Id()
+```

--- a/doc/build/_book/OBITools-V4.epub
+++ b/doc/build/_book/OBITools-V4.epub
--- a/doc/build/_book/annexes.html
+++ b/doc/build/_book/annexes.html
@ -20,6 +20,69 @@ ul.task-list li input[type="checkbox"] {
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@ -215,7 +278,7 @@ ul.task-list li input[type="checkbox"] {
    <h2 id="toc-title">Table of contents</h2>
   
  <ul>
-  <li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">A.0.1</span>  Sequence attributes</a></li>
+  <li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">A.1</span>  Sequence attributes</a></li>
  </ul>
 </nav>
    </div>
@ -239,84 +302,82 @@ ul.task-list li input[type="checkbox"] {

 </header>

-<section id="sequence-attributes" class="level3" data-number="A.0.1">
-<h3 data-number="A.0.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">A.0.1</span> Sequence attributes</h3>
-<section id="reserved-sequence-attributes" class="level4" data-number="A.0.1.1">
-<h4 data-number="A.0.1.1" class="anchored" data-anchor-id="reserved-sequence-attributes"><span class="header-section-number">A.0.1.1</span> Reserved sequence attributes</h4>
-<section id="ali_dir" class="level5" data-number="A.0.1.1.1">
-<h5 data-number="A.0.1.1.1" class="anchored" data-anchor-id="ali_dir"><span class="header-section-number">A.0.1.1.1</span> <code>ali_dir</code></h5>
-<section id="type-string" class="level6" data-number="A.0.1.1.1.1">
-<h6 data-number="A.0.1.1.1.1" class="anchored" data-anchor-id="type-string"><span class="header-section-number">A.0.1.1.1.1</span> Type : <code>string</code></h6>
-<p>The attribute can contain 2 string values <code>"left"</code> or <code>"right".</code></p>
-</section>
-<section id="set-by-the-obipairing-tool" class="level6" data-number="A.0.1.1.1.2">
-<h6 data-number="A.0.1.1.1.2" class="anchored" data-anchor-id="set-by-the-obipairing-tool"><span class="header-section-number">A.0.1.1.1.2</span> Set by the <em>obipairing</em> tool</h6>
+<section id="sequence-attributes" class="level2" data-number="A.1">
+<h2 data-number="A.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">A.1</span> Sequence attributes</h2>
+<p><strong>ali_dir (<code>string</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+<li>The attribute can contain 2 string values <code>left</code> or <code>right</code>.</li>
+</ul>
 <p>The alignment generated by <em>obipairing</em> is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction <code>ali_dir</code> is set to <em>left</em>. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, <code>ali_dir</code> is set to <em>right</em>.</p>
-</section>
-</section>
-<section id="ali_length" class="level5" data-number="A.0.1.1.2">
-<h5 data-number="A.0.1.1.2" class="anchored" data-anchor-id="ali_length"><span class="header-section-number">A.0.1.1.2</span> <code>ali_length</code></h5>
-<section id="set-by-the-obipairing-tool-1" class="level6" data-number="A.0.1.1.2.1">
-<h6 data-number="A.0.1.1.2.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-1"><span class="header-section-number">A.0.1.1.2.1</span> Set by the <em>obipairing</em> tool</h6>
+<p><strong>ali_length (<code>int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+</ul>
 <p>Length of the aligned parts when merging forward and reverse reads</p>
-</section>
-</section>
-<section id="count-the-number-of-sequence-occurrences" class="level5" data-number="A.0.1.1.3">
-<h5 data-number="A.0.1.1.3" class="anchored" data-anchor-id="count-the-number-of-sequence-occurrences"><span class="header-section-number">A.0.1.1.3</span> <code>count</code> : the number of sequence occurrences</h5>
-<section id="set-by-the-obiuniq-tool" class="level6" data-number="A.0.1.1.3.1">
-<h6 data-number="A.0.1.1.3.1" class="anchored" data-anchor-id="set-by-the-obiuniq-tool"><span class="header-section-number">A.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool</h6>
-<p>The <code>count</code> attribute indicates how-many strictly identical sequences have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.</p>
-</section>
-<section id="getter-method-count" class="level6" data-number="A.0.1.1.3.2">
-<h6 data-number="A.0.1.1.3.2" class="anchored" data-anchor-id="getter-method-count"><span class="header-section-number">A.0.1.1.3.2</span> Getter : method <code>Count()</code></h6>
+<p><strong>count (<code>int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obiuniq</em> tool</li>
+<li>Getter : method <code>Count()</code></li>
+<li>Setter : method <code>SetCount(int)</code></li>
+</ul>
+<p>The <code>count</code> attribute indicates how-many strictly identical reads have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.</p>
 <p>The <code>Count()</code> method allows to access to the count attribute as an integer value. If the <code>count</code> attribute is not defined for the given sequence, the value <em>1</em> is returned</p>
-</section>
-</section>
-<section id="merged_" class="level5" data-number="A.0.1.1.4">
-<h5 data-number="A.0.1.1.4" class="anchored" data-anchor-id="merged_"><span class="header-section-number">A.0.1.1.4</span> <code>merged_*</code></h5>
-<section id="type-mapstringint" class="level6" data-number="A.0.1.1.4.1">
-<h6 data-number="A.0.1.1.4.1" class="anchored" data-anchor-id="type-mapstringint"><span class="header-section-number">A.0.1.1.4.1</span> Type : <code>map[string]int</code></h6>
-</section>
-<section id="set-by-the-obiuniq-tool-1" class="level6" data-number="A.0.1.1.4.2">
-<h6 data-number="A.0.1.1.4.2" class="anchored" data-anchor-id="set-by-the-obiuniq-tool-1"><span class="header-section-number">A.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool</h6>
+<p><strong>merged_* (<code>map[string]int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obiuniq</em> tool</li>
+</ul>
 <p>The <code>-m</code> option of the <em>obiuniq</em> tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when <em>obiuniq</em> is run after running <em>obimultiplex</em>. The actual name of the attribute depends on the name of the monitored attribute. If <code>-m</code> option is used with the attribute <em>sample</em>, then this attribute names <em>merged_sample</em>.</p>
-</section>
-</section>
-<section id="mode" class="level5" data-number="A.0.1.1.5">
-<h5 data-number="A.0.1.1.5" class="anchored" data-anchor-id="mode"><span class="header-section-number">A.0.1.1.5</span> <code>mode</code></h5>
-<section id="set-by-the-obipairing-tool-2" class="level6" data-number="A.0.1.1.5.1">
-<h6 data-number="A.0.1.1.5.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-2"><span class="header-section-number">A.0.1.1.5.1</span> Set by the <em>obipairing</em> tool</h6>
-<p><strong><code>obitag_ref_index</code></strong></p>
-</section>
-<section id="set-by-the-obirefidx-tool." class="level6" data-number="A.0.1.1.5.2">
-<h6 data-number="A.0.1.1.5.2" class="anchored" data-anchor-id="set-by-the-obirefidx-tool."><span class="header-section-number">A.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.</h6>
+<p><strong>mode (<code>string</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+<li>The attribute can contain 2 string values <code>join</code> or <code>alignment</code>.</li>
+</ul>
+<p><strong>obitag_ref_index (<code>map[string]string</code>)</strong></p>
+<ul>
+<li>Set by the <em>obirefidx</em> tool.</li>
+</ul>
 <p>It resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.</p>
-</section>
-<section id="getter-method-count-1" class="level6" data-number="A.0.1.1.5.3">
-<h6 data-number="A.0.1.1.5.3" class="anchored" data-anchor-id="getter-method-count-1"><span class="header-section-number">A.0.1.1.5.3</span> Getter : method <code>Count()</code></h6>
-</section>
-</section>
-<section id="pairing_mismatches" class="level5" data-number="A.0.1.1.6">
-<h5 data-number="A.0.1.1.6" class="anchored" data-anchor-id="pairing_mismatches"><span class="header-section-number">A.0.1.1.6</span> <code>pairing_mismatches</code></h5>
-<section id="set-by-the-obipairing-tool-3" class="level6" data-number="A.0.1.1.6.1">
-<h6 data-number="A.0.1.1.6.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-3"><span class="header-section-number">A.0.1.1.6.1</span> Set by the <em>obipairing</em> tool</h6>
-</section>
-</section>
-<section id="score" class="level5" data-number="A.0.1.1.7">
-<h5 data-number="A.0.1.1.7" class="anchored" data-anchor-id="score"><span class="header-section-number">A.0.1.1.7</span> <code>score</code></h5>
-<section id="set-by-the-obipairing-tool-4" class="level6" data-number="A.0.1.1.7.1">
-<h6 data-number="A.0.1.1.7.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-4"><span class="header-section-number">A.0.1.1.7.1</span> Set by the <em>obipairing</em> tool</h6>
-</section>
-</section>
-<section id="score_norm" class="level5" data-number="A.0.1.1.8">
-<h5 data-number="A.0.1.1.8" class="anchored" data-anchor-id="score_norm"><span class="header-section-number">A.0.1.1.8</span> <code>score_norm</code></h5>
-<section id="set-by-the-obipairing-tool-5" class="level6" data-number="A.0.1.1.8.1">
-<h6 data-number="A.0.1.1.8.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-5"><span class="header-section-number">A.0.1.1.8.1</span> Set by the <em>obipairing</em> tool</h6>
+<div class="sourceCode" id="cb1"><pre class="sourceCode json code-with-copy"><code class="sourceCode json"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>   <span class="fu">{</span><span class="dt">"0"</span><span class="fu">:</span><span class="st">"9606@Homo sapiens@species"</span><span class="fu">,</span></span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"2"</span><span class="fu">:</span><span class="st">"207598@Homininae@subfamily"</span><span class="fu">,</span></span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"3"</span><span class="fu">:</span><span class="st">"9604@Hominidae@family"</span><span class="fu">,</span></span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"8"</span><span class="fu">:</span><span class="st">"314295@Hominoidea@superfamily"</span><span class="fu">,</span></span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"10"</span><span class="fu">:</span><span class="st">"9526@Catarrhini@parvorder"</span><span class="fu">,</span></span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"12"</span><span class="fu">:</span><span class="st">"1437010@Boreoeutheria@clade"</span><span class="fu">,</span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"16"</span><span class="fu">:</span><span class="st">"9347@Eutheria@clade"</span><span class="fu">,</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"17"</span><span class="fu">:</span><span class="st">"40674@Mammalia@class"</span><span class="fu">,</span></span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"22"</span><span class="fu">:</span><span class="st">"117571@Euteleostomi@clade"</span><span class="fu">,</span></span>
+<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"25"</span><span class="fu">:</span><span class="st">"7776@Gnathostomata@clade"</span><span class="fu">,</span></span>
+<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"29"</span><span class="fu">:</span><span class="st">"33213@Bilateria@clade"</span><span class="fu">,</span></span>
+<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>    <span class="dt">"30"</span><span class="fu">:</span><span class="st">"6072@Eumetazoa@clade"</span><span class="fu">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p><strong>pairing_mismatches (<code>map[string]string</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+</ul>
+<p><strong>seq_a_single (<code>int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+</ul>
+<p><strong>seq_ab_match (<code>int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+</ul>
+<p><strong>seq_b_single (<code>int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+</ul>
+<p><strong>score (<code>int</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+</ul>
+<p><strong>score_norm (<code>float</code>)</strong></p>
+<ul>
+<li>Set by the <em>obipairing</em> tool</li>
+<li>The value ranges between 0 and 1.</li>
+</ul>
+<p>Score of the alignment between forward and reverse reads expressed as a fraction of identity.</p>


-</section>
-</section>
-</section>
 </section>

 </main> <!-- /main -->
--- a/doc/build/_book/comm_sampling.html
+++ b/doc/build/_book/comm_sampling.html
@ -314,6 +314,23 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
 <section id="selecting-sequences-based-on-their-caracteristics" class="level4" data-number="12.1.1.1">
 <h4 data-number="12.1.1.1" class="anchored" data-anchor-id="selecting-sequences-based-on-their-caracteristics"><span class="header-section-number">12.1.1.1</span> Selecting sequences based on their caracteristics</h4>
 <p>Sequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.</p>
+<p><strong>Selection based on the sequence</strong></p>
+<p>Sequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (<em>e.g</em> <code>AACCTT</code>). But the usage of regular patterns allows for looking for more complex pattern. As example, <code>A[TG]C+G</code> matches a <code>A</code>, followed by a <code>T</code> or a <code>G</code>, then one or several <code>C</code> and endly a <code>G</code>.</p>
+<dl>
+<dt><strong>--sequence</strong>|<strong>-s</strong> <em>PATTERN</em></dt>
+<dd>
+<p>Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available <a href="https://yourbasic.org/golang/regexp-cheat-sheet/#cheat-sheet">here</a>.</p>
+</dd>
+<dt><em>Examples:</em></dt>
+<dd>
+<p>Selects only the sequence records that contain an <em>EcoRI</em> restriction site.</p>
+</dd>
+</dl>
+<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'GAATTC'</span> seq1.fasta <span class="op">&gt;</span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>: Selects only the sequence records that contain a stretch of at least 10 <code>A</code>.</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'A{10,}'</span> seq1.fasta <span class="op">&gt;</span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>: Selects only the sequence records that do not contain ambiguous nucleotides.</p>
+<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'^[ACGT]+$'</span> seq1.fasta <span class="op">&gt;</span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <dl>
 <dt><strong>--min-count</strong> | <strong>-c</strong> <em>COUNT</em></dt>
 <dd>
@ -323,12 +340,12 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
 <dd>
 <p>only sequences reprensenting no more than <em>COUNT</em> reads will be selected. That option rely on the <code>count</code> attribute. If the <code>count</code> attribute is not defined for a sequence record, it is assumed equal to <span class="math inline">\(1\)</span>.</p>
 </dd>
-<dt>Example</dt>
+<dt><em>Examples</em></dt>
 <dd>
 <p>Selecting sequence records representing at least five reads in the dataset.</p>
 </dd>
 </dl>
-<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-c</span> 5 data_SPER01.fasta <span class="op">&gt;</span> data_norare_SPER01.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-c</span> 5 data_SPER01.fasta <span class="op">&gt;</span> data_norare_SPER01.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>


 </section>
--- a/doc/build/_book/expressions.html
+++ b/doc/build/_book/expressions.html
@ -124,6 +124,7 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
  }
 }</script>

+  <script src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js" type="text/javascript"></script>

 </head>

@ -284,6 +285,8 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
  <li><a href="#instrospection-functions" id="toc-instrospection-functions" class="nav-link" data-scroll-target="#instrospection-functions">Instrospection functions</a></li>
  <li><a href="#cast-functions" id="toc-cast-functions" class="nav-link" data-scroll-target="#cast-functions">Cast functions</a></li>
  <li><a href="#string-related-functions" id="toc-string-related-functions" class="nav-link" data-scroll-target="#string-related-functions">String related functions</a></li>
+  <li><a href="#condition-function" id="toc-condition-function" class="nav-link" data-scroll-target="#condition-function">Condition function</a></li>
+  <li><a href="#sequence-analysis-related-function" id="toc-sequence-analysis-related-function" class="nav-link" data-scroll-target="#sequence-analysis-related-function"><span class="toc-section-number">7.2.1</span>  Sequence analysis related function</a></li>
  </ul></li>
  <li><a href="#accessing-to-the-sequence-annotations" id="toc-accessing-to-the-sequence-annotations" class="nav-link" data-scroll-target="#accessing-to-the-sequence-annotations"><span class="toc-section-number">7.3</span>  Accessing to the sequence annotations</a></li>
  </ul>
@ -321,24 +324,67 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
 <h2 data-number="7.2" class="anchored" data-anchor-id="function-defined-in-the-language"><span class="header-section-number">7.2</span> Function defined in the language</h2>
 <section id="instrospection-functions" class="level3 unnumbered">
 <h3 class="unnumbered anchored" data-anchor-id="instrospection-functions">Instrospection functions</h3>
-<ul>
-<li><code>len(x)</code>is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like <code>annotations</code>, the number of elements in an array. The reurned value is an <code>int</code>.</li>
-</ul>
+<dl>
+<dt><strong><code>len(x)</code></strong></dt>
+<dd>
+<p>It is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like <code>annotations</code>, the number of elements in an array. The reurned value is an <code>int</code>.</p>
+</dd>
+</dl>
 </section>
 <section id="cast-functions" class="level3 unnumbered">
 <h3 class="unnumbered anchored" data-anchor-id="cast-functions">Cast functions</h3>
-<ul>
-<li><code>int(x)</code> converts if possible the <code>x</code> value to an integer value. The function returns an <code>int</code>.</li>
-<li><code>numeric(x)</code> converts if possible the <code>x</code> value to a float value. The function returns a <code>float</code>.</li>
-<li><code>bool(x)</code> converts if possible the <code>x</code> value to a boolean value. The function returns a <code>bool</code>.</li>
-</ul>
+<dl>
+<dt><strong><code>int(x)</code></strong></dt>
+<dd>
+<p>Converts if possible the <code>x</code> value to an integer value. The function returns an <code>int</code>.</p>
+</dd>
+<dt><strong><code>numeric(x)</code></strong></dt>
+<dd>
+<p>Converts if possible the <code>x</code> value to a float value. The function returns a <code>float</code>.</p>
+</dd>
+<dt><strong><code>bool(x)</code></strong></dt>
+<dd>
+<p>Converts if possible the <code>x</code> value to a boolean value. The function returns a <code>bool</code>.</p>
+</dd>
+</dl>
 </section>
 <section id="string-related-functions" class="level3 unnumbered">
 <h3 class="unnumbered anchored" data-anchor-id="string-related-functions">String related functions</h3>
-<ul>
-<li><code>printf(format,...)</code> allows to combine several values to build a string. <code>format</code> follows the classical C <code>printf</code> syntax. The function returns a <code>string</code>.</li>
-<li><code>subspc(x)</code> substitutes every space in the <code>x</code> string by the underscore (<code>_</code>) character. The function returns a <code>string</code>.</li>
-</ul>
+<dl>
+<dt><strong><code>printf(format,...)</code></strong></dt>
+<dd>
+<p>Allows to combine several values to build a string. <code>format</code> follows the classical C <code>printf</code> syntax. The function returns a <code>string</code>.</p>
+</dd>
+<dt><strong><code>subspc(x)</code></strong></dt>
+<dd>
+<p>substitutes every space in the <code>x</code> string by the underscore (<code>_</code>) character. The function returns a <code>string</code>.</p>
+</dd>
+</dl>
+</section>
+<section id="condition-function" class="level3 unnumbered">
+<h3 class="unnumbered anchored" data-anchor-id="condition-function">Condition function</h3>
+<dl>
+<dt><strong><code>ifelse(condition,val1,val2)</code></strong></dt>
+<dd>
+<p>The <code>condition</code> value has to be a <code>bool</code> value. If it is <code>true</code> the function returns <code>val1</code>, otherwise, it is returning <code>val2</code>.</p>
+</dd>
+</dl>
+</section>
+<section id="sequence-analysis-related-function" class="level3" data-number="7.2.1">
+<h3 data-number="7.2.1" class="anchored" data-anchor-id="sequence-analysis-related-function"><span class="header-section-number">7.2.1</span> Sequence analysis related function</h3>
+<dl>
+<dt><strong><code>composition(sequence)</code></strong></dt>
+<dd>
+<p>The nucleotide composition of the sequence is returned as as map indexed by <code>a</code>, <code>c</code>, <code>g</code>, or <code>t</code> and each value is the number of occurrences of that nucleotide. A fifth key <code>others</code> accounts for all others symboles.</p>
+</dd>
+<dt><strong><code>gcskew(sequence)</code></strong></dt>
+<dd>
+<p>Computes the excess of g compare to c of the sequence, known as the GC skew.</p>
+<p><span class="math display">\[
+Skew_{GC}=\frac{G-C}{G+C}
+\]</span></p>
+</dd>
+</dl>
 </section>
 </section>
 <section id="accessing-to-the-sequence-annotations" class="level2" data-number="7.3">
@ -352,6 +398,7 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
 <li>The sequence identifier : <code>Id()</code></li>
 <li>THe sequence definition : <code>Definition()</code></li>
 </ul>
+<div class="sourceCode" id="cb3"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>sequence<span class="op">.</span>Id<span class="op">()</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>


 </section>
--- a/doc/build/_man/man1/obigrep.man
+++ b/doc/build/_man/man1/obigrep.man
@ -174,14 +174,22 @@ selected.
 That option rely on the \f[V]count\f[R] attribute.
 If the \f[V]count\f[R] attribute is not defined for a sequence record,
 it is assumed equal to 1.
-.PP
+.TP
 \f[B]--max-length\f[R] | \f[B]-L\f[R] \f[I]LENGTH\f[R]
-.PP
+Keeps sequence records whose sequence length is equal or shorter than
+\f[I]LENGTH\f[R].
+.TP
 \f[B]--min-length\f[R] | \f[B]-l\f[R] \f[I]LENGTH\f[R]
+Keeps sequence records whose sequence length is equal or longer than
+\f[I]LENGTH\f[R].
 .PP
 \f[B]--predicate\f[R]|\f[B]-p\f[R] \f[I]EXPRESSION\f[R]
-.PP
+.TP
 \f[B]--sequence\f[R]|\f[B]-s\f[R] \f[I]PATTERN\f[R]
+Regular expression pattern to be tested against the sequence itself.
+The pattern is case insensitive.
+A complete description of the regular pattern grammar is available
+here (https://yourbasic.org/golang/regexp-cheat-sheet/#cheat-sheet).
 .PP
 \f[B]--inverse-match\f[R] | \f[B]-v\f[R]
 .PP
--- a/doc/lib/options/selection/_max-length.qmd
+++ b/doc/lib/options/selection/_max-length.qmd
@ -0,0 +1,3 @@
+**\--max-length** | **-L** _LENGTH_
+
+: Keeps sequence records whose sequence length is equal or shorter than _LENGTH_.
--- a/doc/lib/options/selection/_min-length.qmd
+++ b/doc/lib/options/selection/_min-length.qmd
@ -0,0 +1,3 @@
+**\--min-length** | **-l** _LENGTH_
+
+: Keeps sequence records whose sequence length is equal or longer than _LENGTH_.
--- a/doc/lib/options/selection/_sequence.qmd
+++ b/doc/lib/options/selection/_sequence.qmd
@ -0,0 +1,7 @@
+**\--sequence**|**-s** _PATTERN_
+
+: Regular expression pattern to be tested against the
+  sequence itself. The pattern is case insensitive. A
+  complete description of the regular pattern grammar
+  is available [here](https://yourbasic.org/golang/regexp-cheat-sheet/#cheat-sheet).
+  
--- a/doc/man/obigrep.qmd
+++ b/doc/man/obigrep.qmd
@ -99,13 +99,13 @@ The OBITools are centered around the [FASTA] (https://en.wikipedia.org/wiki/FAST

 {{< include ../lib/options/selection/_min-count.qmd >}}

-**\--max-length** | **-L** _LENGTH_
+{{< include ../lib/options/selection/_max-length.qmd >}}

-**\--min-length** | **-l** _LENGTH_
+{{< include ../lib/options/selection/_min-length.qmd >}}

 **\--predicate**|**-p** _EXPRESSION_

-**\--sequence**|**-s** _PATTERN_
+{{< include ../lib/options/selection/_sequence.qmd >}}

 **\--inverse-match** | **-v**